Package: decontX 1.3.0

Yuan Yin

decontX: Decontamination of single cell genomics data

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

Authors:Yuan Yin [aut, cre], Masanao Yajima [aut], Joshua Campbell [aut]

decontX_1.3.0.tar.gz
decontX_1.3.0.zip(r-4.5)decontX_1.3.0.zip(r-4.4)decontX_1.3.0.zip(r-4.3)
decontX_1.3.0.tgz(r-4.4-arm64)decontX_1.3.0.tgz(r-4.4-x86_64)decontX_1.3.0.tgz(r-4.3-arm64)decontX_1.3.0.tgz(r-4.3-x86_64)
decontX_1.3.0.tar.gz(r-4.5-noble)decontX_1.3.0.tar.gz(r-4.4-noble)
decontX.pdf |decontX.html✨
decontX/json (API)
NEWS

# Install 'decontX' in R:

install.packages('decontX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:decontX-1.3.0(bioc 3.20)decontX-1.2.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

11 exports 0.82 score 228 dependencies

Last updated 2 months agofrom:5d43c57ad1

Exports:decontPro decontX decontXcounts decontXcounts<-plotBoxByCluster plotDecontXContamination plotDecontXMarkerExpression plotDecontXMarkerPercentage plotDensity retrieveFeatureIndex simulateContamination

Dependencies:abind askpass backports base64enc beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bitops bluster bslib cachem Cairo callr caTools celda checkmate circlize cli clue cluster codetools colorspace combinat commonmark ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table dbscan DelayedArray DelayedMatrixStats deldir desc digest distributional doParallel dotCall64 dplyr dqrng edgeR enrichR evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggbeeswarm ggplot2 ggrastr ggrepel ggridges GlobalOptions globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph inline IRanges irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval leiden lifecycle limma listenv lmtest locfit loo magrittr MASS Matrix MatrixGenerics matrixStats MCMCprecision memoise metapod mgcv mime miniUI munsell nlme numDeriv openssl parallelly patchwork pbapply pheatmap pillar pkgbuild pkgconfig plotly plyr png polyclip posterior processx progressr promises ps purrr QuickJSR R6 ragg RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppParallel RcppProgress RcppTOML reshape2 reticulate rjson rlang rmarkdown ROCR rprojroot RSpectra rstan rstantools rsvd Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scattermore scran sctransform scuttle Seurat SeuratObject shape shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils StanHeaders statmod stringi stringr SummarizedExperiment survival sys systemfonts tensor tensorA textshaping tibble tidyr tidyselect tinytex UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr WriteXLS xfun xtable XVector yaml zlibbioc zoo

Decontamination of single cell protein expression data with DecontPro

Yuan Yin, Joshua Campbell

Rendered fromdecontPro.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-21
Started: 2023-02-22

Decontamination of ambient RNA in single-cell genomic data with DecontX

Shiyi (Iris) Yang, Zhe Wang, Yuan Yin, Joshua Campbell

Rendered fromdecontX.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-21
Started: 2023-03-01

Help page	Topics
The 'decontX' package.	decontX-package
Call Stan variational bayes for inference	.call_stan_vb
Process Stan output.	.process_stan_vb_out
Decontaminate using decontPro	decontPro decontPro,ANY-method decontPro,Seurat-method decontPro,SingleCellExperiment-method
Contamination estimation with decontX	decontX decontX,ANY-method decontX,SingleCellExperiment-method
Get or set decontaminated counts matrix	decontXcounts decontXcounts,SingleCellExperiment-method decontXcounts<- decontXcounts<-,SingleCellExperiment-method
Fast normalization for numeric matrix	fastNormProp
Fast normalization for numeric matrix	fastNormPropLog
Fast normalization for numeric matrix	fastNormPropSqrt
get row and column indices of none zero elements in the matrix	nonzero
Boxplot of features grouped by cell type	plotBoxByCluster
Plots contamination on UMAP coordinates	plotDecontXContamination
Plots expression of marker genes before and after decontamination	plotDecontXMarkerExpression
Plots percentage of cells cell types expressing markers	plotDecontXMarkerPercentage
Density of each ADT, raw counts overlapped with decontaminated counts	plotDensity
Retrieve row index for a set of features	retrieveFeatureIndex
Simulate contaminated count matrix	simulateContamination

Package: decontX 1.3.0

decontX: Decontamination of single cell genomics data

Decontamination of single cell protein expression data with DecontPro

Decontamination of ambient RNA in single-cell genomic data with DecontX

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)